https://github.com/athos/igv-client

Clojure implementation of IGV client to control IGV via its Port Commands
https://github.com/athos/igv-client

clojure igv

Last synced: about 1 month ago
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Clojure implementation of IGV client to control IGV via its Port Commands

• Host: GitHub
• URL: https://github.com/athos/igv-client
• Owner: athos
• License: epl-2.0
• Created: 2019-01-18T06:48:35.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2023-11-20T21:15:22.000Z (about 1 year ago)
• Last Synced: 2024-08-16T16:24:15.651Z (4 months ago)
• Topics: clojure, igv
• Language: Clojure
• Size: 16.6 KB
• Stars: 4
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

        
# igv-client

[![Clojars Project](https://img.shields.io/clojars/v/igv-client.svg)](https://clojars.org/igv-client)

[![CircleCI](https://circleci.com/gh/athos/igv-client.svg?style=shield)](https://circleci.com/gh/athos/igv-client)

Clojure implementation of IGV client to control [IGV](http://software.broadinstitute.org/software/igv/) via its [Port Commands](https://igv.org/doc/desktop/#UserGuide/advanced/external_control/#port-commands)

## Installation

Add the following to your `:dependencies`:

[![Clojars Project](https://clojars.org/igv-client/latest-version.svg)](https://clojars.org/igv-client)

## Usage

```clojure

(require '[igv-client.core :as igv])

(def client (igv/connect "127.0.0.1" 60151))

(igv/set-snapshot-dir! client "/path/to/snapshot/dir")

(igv/reset client)

(igv/load-file client "/path/to/your/input/file")

(igv/goto client "chr1" 123456)

(igv/collapse client)

(igv/snapshot client)

(.close client)

;; or you can also write the same thing with the threading macro:

(-> client

    igv/reset

    (igv/load-file "/path/to/your/input/file")

    (igv/goto "chr1" 123456)

    igv/collapse

    igv/snapshot

    .close)

```

## Available Commands

Following is the list of commands available:

| Command Name          | Function Signature                      |

|-----------------------|-----------------------------------------|

| `version`             | `(version )`                    |

| `new`/`reset`/`clear` | `(reset )`                      |

| `load`/`loadfile`     | `(load-file  )`           |

| `remove`              | `(remove  )`             |

| `genome`              | `(genome  )`            |

| `goto`                | `(goto  )`               |

|                       | `(goto   )`           |

| `gototrack`           | `(goto-track  )`         |

| `setsleepinterval`    | `(set-sleep-interval!  )` |

| `snapshotdirectory`   | `(set-snapshot-dir!  )`    |

| `snapshot`            | `(snapshot )`                   |

| `zoomin`              | `(zoom-in )`                    |

| `zoomout`             | `(zoom-out )`                   |

| `collapse`            | `(collapse  [])`         |

| `expand`              | `(expand  [])`           |

| `squish`              | `(squish  [])`           |

| `tofront`             | `(bring-to-front! )`            |

## License

Copyright © 2019 Shogo Ohta

This program and the accompanying materials are made available under the

terms of the Eclipse Public License 2.0 which is available at

http://www.eclipse.org/legal/epl-2.0.

This Source Code may also be made available under the following Secondary

Licenses when the conditions for such availability set forth in the Eclipse

Public License, v. 2.0 are satisfied: GNU General Public License as published by

the Free Software Foundation, either version 2 of the License, or (at your

option) any later version, with the GNU Classpath Exception which is available

at https://www.gnu.org/software/classpath/license.html.